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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctaaaaaacaagtgggagtgtattagcatccaaatgcattagttagagttcatgtgcctgtaaaacatccattaatattgtgcatattgattgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAGCATGAGTTGGTTTTAGGTATCATTGATTTTATGAGGCAGTATACATGGG

Basic information

species Glycine max
transcript GLYMA13G17510.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G17510.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os08g34950.1 (Oryza sativa), 3'ss of exon 10
----cctaaaaaacaagtggg---agtgtattagcatccaaatgcattagttagagttcatgtgcctgtaaaacatccattaatattgtgcatattgattgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAGCATGAGTTGGTTTTAGGTATCATTGATTTTATGAGGCAGTATACATGGG
      ||  | ||| |  |      | ||||     |||   |||  | |     |  || | |   ||  ||   |||||||   || | | |    | ||| ||  |||  |||||||||| ||||||||||| || || || || ||||| || ||||| |||||| | || || ||||||||||||||||||||||||||||
agggtttatgagacaggctgataagatttattgcaggccagtagcagcattcgatat--atcttctcatatgac--tcattaatgaagt-cttgtc--ctcttgtagGGAATTGATGTGATGGATTACTCATTGCTTGTGGGAGTTGACGAGGAGAAACATGAATTGGTTCTGGGAATAATTGATTTTATGAGGCAGTATACATGGG

upper sequence: GLYMA13G17510.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G153722_T01 (Zea mays), 3'ss of exon 10
cctaaaaaacaagtgggagtgtattagcatccaaatgcattagttagagttca-tgtgcctgtaaaacatcca---ttaatattgtgcatattgat-tgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAGCATGAGTTGGTTTTAGGTATCATTGATTTTATGAGGCAGTATACATGGG
        |    |   ||| |||   | |  || |  |   ||||   ||   |||     || ||  |  |   ||||   |||        || | || |||  |||  ||||||||||||| || ||||| || || || || ||||| || |||||  |||| ||||| || ||||||||||||||||||||||||||||
---tgctgatgcttccaagtttatcttcttgtaactata--ggttacctttttctgttttcttataatctgtaggcttaactctgtaggctcccatgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAACATGAACTGGTCTTAGGAATTATTGATTTTATGAGGCAGTATACATGGG

upper sequence: GLYMA13G17510.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0016g00360.t01 (Vitis vinifera), 3'ss of exon 13
---cctaaaaaacaagtgggagtgtattagcatccaaatgcattagttagagttcatgtgcctgtaaaacatccattaatattgtgcatattgattgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAGCATGAGTTGGTTTTAGGTATCATTGATTTTATGAGGCAGTATACATGGG
      |   | |   |   |     || |       |   | |  ||  || |  | |   | || |   |   ||  |||  |   | |   || || ||||| ||| |||| |||||||||||||| |||||||| ||||||||||||||||||||  ||||  | || || || || |||||| |||| ||||| ||||
aaattgacctaccttctcaaaagcccttggtcaatgcaaataatgtttcaagattctcttgttatagactctaatttgttatcat---tttatgttctttcagTCGATAGATGTAATGGACTACTCATTACTGGTTGGGGTGGATGAGGAAAAGCATGAACTGGTCCTTGGGATAATCGACTTTATGCGGCAATATACCTGGG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|11412624|gb|BF424635.1|BF424635
EST:     CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCA                         TCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
genomic: CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCAgtaagtctga ... attgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
EST: gi|192332689|gb|FK025346.1|FK025346
EST:     CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCA                         TCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
genomic: CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCAgtaagtctga ... attgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
EST: gi|31310487|gb|CD395690.1|CD395690
EST:     GTGGAATGATACTGCCTTCCTTGCA                         TCAATATATGTGATGGACTACTCATTGCTGGTTGGCTTGGATGAGGAAAAG
genomic: GTGGAATGATACTGCCTTCCTTGCAgtaagtctga ... attgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
EST: gi|254333966|gb|GR848884.1|GR848884
EST:     CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCA                         TCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
genomic: CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCAgtaagtctga ... attgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
EST: gi|193552188|gb|FK510275.1|FK510275
EST:     CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCA                         TCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
genomic: CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCAgtaagtctga ... attgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
EST: gi|192332690|gb|FK025347.1|FK025347
EST:     CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCA                         TCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
genomic: CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCAgtaagtctga ... attgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG
EST: gi|18040859|gb|BM309153.1|BM309153
EST:     CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCA                         TCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGANGAAAAG
genomic: CAAAACGGTTGCTCGAGAGGGCTGTGTGGAATGATACTGCCTTCCTTGCAgtaagtctga ... attgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagttcatgtgcctgtaaaacatccattaatattgtgcatattgattgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAGCATGAGTTGGTTTTAGGTATCATTGATTTTATGAGGCAGTATACATGGG
                                        tattgat  putative branch site (score: 3)
                          attaatattgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctaaaaaacaagtgggagtgtattagcatccaaatgcattagttagagttcatgtgcctgtaaaacatccattaatattgtgcatattgattgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAGCATGAGTTGGTTTTAGGTATCATTGATTTTATGAGGCAGTATACATGGG

- taaaaaa
- - - - - - - gggagtg
- - - - - - - - - - - - - gcatcca
- - - - - - - - - - - - - - - - - -tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - -catgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatat